Another tricky word you will encounter soon --
"в" + "час" = "в часу"
- в котором часу она проснулась?
But suddenly, speaking figuratively (not about specific point in time, but of some more prolonged "times"), we are again on the light side:
- в час опасности, в недобрый час, ...

Another simple question here: Whenever I see questions asking "on which day?" I see it printed as «в какой день?» But if день is a masculine noun shouldn't it be «в каком день?»

Any help is appreciated.

This is the Accusative case.

We use different structures for different periods of time in Russian, there is no particular logic in it. (Basically it is the same in English - they say 'On Monday', but 'in Summer', but 'at night' - no logic really)

And, of course, questions usually have the same structure as answers. This is the basic rule for Russian, English and most other languages I believe.

So what we have in Russian.

Dates
Genitive case with no preposition: Восьмого октября, пятого марта. And the question is alson in Genitive: Какого числа?

Days of the week
В + Accusative: В понедельник, в среду.So the question is also in Accusative: В какой день (недели)?

Basically this is the answer to your question. As you may see, nothing really complicated, just something you need to learn and remember.

However, sometimes, the questions do not match the structure of answers if we talk about Seasons and Parts of 24Hours
We use Instrumental case for them: ночью, утром, летом, зимой. But the questions will be В + Accusative: В какое время года? В какое время суток?